BN1430 Genetic Spatial Mapping Report

Genetic Spatial Mapping Plot

This plot shows the spatial genetic mapping results across different tissues.

Cauchy Combination Result

This table presents the results of the Cauchy combination test, summarizing the genetic associations.

Annotation P Cauchy P Median
Layer 3 4.6517e-08 4.5637e-05
Layer 4 6.3336e-08 2.8177e-06
Layer 5 6.6293e-07 1.3192e-04
Layer 6 7.2926e-06 4.1590e-02
Layer 2 1.2338e-05 3.3638e-03
Layer 1 9.5447e-01 7.6648e-01
WM 9.9569e-01 2.9303e-01

Diagnosis Manhattan Plot

The Manhattan plot shows the association of SNPs with the top associated gene across the genome.

Gene Expression and GSS Distribution

Select a gene to view its expression distribution and gene specificity score (GSS).

Expression Distribution
PRPF19 Expression Distribution
Gene Specificity Score (GSS)
PRPF19 GSS Distribution

Top 50 Gene Diagnostic Info

This table lists the top 50 genes based on diagnostic criteria, including the gene specificity score (GSS) and PCC.

Gene Annotation Median GSS PCC
PRPF19 Layer 4 3.0312 0.8603
DIRAS1 Layer 4 3.3945 0.8547
TRIM37 Layer 4 3.2148 0.8531
KCNA2 Layer 4 3.9375 0.8469
CLSTN3 Layer 4 3.2012 0.8469
KLC2 Layer 4 2.7129 0.8467
GABBR2 Layer 4 3.4531 0.8455
RIMS3 Layer 4 3.4453 0.8448
NMNAT2 Layer 4 3.0449 0.8445
FGF12 Layer 4 3.4004 0.8435
PNMA8B Layer 4 3.0527 0.8407
CPLX1 Layer 4 3.3496 0.8405
ADGRL1 Layer 4 2.9473 0.8398
KIAA0408 Layer 4 3.0527 0.8392
GPRASP1 Layer 4 2.9668 0.8383
ATXN7L3 Layer 3 2.7852 0.8382
RBFOX2 Layer 4 3.5059 0.8380
EPHA4 Layer 4 3.2715 0.8366
KIAA1191 Layer 4 2.7793 0.8366
SCN8A Layer 3 3.2637 0.8362
SLC6A17 Layer 4 3.1875 0.8361
TSC22D3 Layer 4 2.7715 0.8360
VDAC3 Layer 4 2.7715 0.8358
GOT1 Layer 4 2.9805 0.8356
PPME1 Layer 4 2.9082 0.8344
KCNC2 Layer 4 3.8965 0.8344
AAK1 Layer 4 2.9863 0.8335
EPHB6 Layer 4 3.2500 0.8334
RNPS1 Layer 4 2.7539 0.8330
ETS2 Layer 3 2.7852 0.8330
RNF208 Layer 4 2.8594 0.8329
VPS4A Layer 4 2.8223 0.8328
MAT2B Layer 4 3.2363 0.8327
NUAK1 Layer 4 3.4238 0.8326
NEUROD2 Layer 4 3.2578 0.8326
CSRNP3 Layer 4 2.9531 0.8325
MAP9 Layer 4 3.3066 0.8325
PLCB1 Layer 3 3.1113 0.8323
ADAR Layer 4 2.7910 0.8323
CNTNAP2 Layer 4 3.5508 0.8323
CHD5 Layer 4 3.5586 0.8315
HDGFL3 Layer 4 2.7656 0.8315
PSMA4 Layer 4 2.5840 0.8313
FAM81A Layer 3 2.8398 0.8310
PPFIA3 Layer 4 2.9805 0.8309
COX7A2L Layer 4 2.7969 0.8307
WDR82 Layer 4 2.8965 0.8303
SCN2B Layer 5 2.7656 0.8301
CD99L2 Layer 4 3.1602 0.8298
TXNL1 Layer 4 2.7480 0.8297

Running Info

Click to view detailed run information and parameters.

gsMap Version: 1.73.0

Parameters:

  • Sample Name: BN1430
  • Trait Name: PD
  • Summary Statistics File: /mnt/data/projects/ASAP/ST/gsMAP/GWAS_nallsEtAl2019_allSamples_allVariants.sumstats.gz
  • HDF5 Path: /mnt/data/projects/ASAP/ST/gsMAP/st_anndata_h5ads/st_adata_BN1430_for_gsmap.h5ad
  • Annotation: smoothed_label_s5
  • Spatial LDSC Save Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1430/spatial_ldsc
  • Cauchy Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1430/cauchy_combination
  • Report Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1430/report/PD
  • gsMap Report File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1430/report/PD/BN1430_PD_gsMap_Report.html
  • Gene Diagnostic Info File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1430/report/PD/BN1430_PD_Gene_Diagnostic_Info.csv
  • Report Generation Date: 2025-04-11 04:18:20
  • Number of Processes: 10
  • Spending Time: 0h 4m